1wpp

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(New page: 200px<br /><applet load="1wpp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wpp, resolution 2.05&Aring;" /> '''Structure of Strepto...)
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[[Image:1wpp.jpg|left|200px]]<br /><applet load="1wpp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wpp, resolution 2.05&Aring;" />
 
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'''Structure of Streptococcus gordonii inorganic pyrophosphatase'''<br />
 
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==Overview==
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==Structure of Streptococcus gordonii inorganic pyrophosphatase==
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Family II inorganic pyrophosphatases (PPases) constitute a new, evolutionary group of PPases, with a different fold and mechanism than the, common family I enzyme; they are related to the "DHH" family of, phosphoesterases. Biochemical studies have shown that Mn(2+) and Co(2+), preferentially activate family II PPases; Mg(2+) partially activates; and, Zn(2+) can either activate or inhibit (Zyryanov et al., Biochemistry, 43, 14395-14402, accompanying paper in this issue). The three solved family II, PPase structures did not explain the differences between the PPase, families nor the metal ion differences described above. We therefore, solved three new family II PPase structures: Bacillus subtilis PPase, (Bs-PPase) dimer core bound to Mn(2+) at 1.3 A resolution, and, at 2.05 A, resolution, metal-free Bs-PPase and Streptococcus gordonii (Sg-PPase), containing sulfate and Zn(2+). Comparison of the new and old structures of, various family II PPases demonstrates why the family II enzyme prefers, Mn(2+) or Co(2+), as an activator rather than Mg(2+). Both M1 and M2, undergo significant changes upon substrate binding, changing from, five-coordinate to octahedral geometry. Mn(2+) and Co(2+), which readily, adopt different coordination states and geometries, are thus favored., Combining our structures with biochemical data, we identified M2 as the, high-affinity metal site. Zn(2+) activates in the M1 site, where, octahedral geometry is not essential for catalysis, but inhibits in the M2, site, because it is unable to assume octahedral geometry but remains, trigonal bipyramidal. Finally, we propose that Lys205-Gln81-Gln80 form a, hydrophilic channel to speed product release from the active site.
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<StructureSection load='1wpp' size='340' side='right'caption='[[1wpp]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1wpp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_gordonii_str._Challis Streptococcus gordonii str. Challis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPP FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wpp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpp OCA], [https://pdbe.org/1wpp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpp RCSB], [https://www.ebi.ac.uk/pdbsum/1wpp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpp ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PPAC_STRGC PPAC_STRGC]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wp/1wpp_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wpp ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1WPP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_gordonii_str._challis Streptococcus gordonii str. challis] with ZN, SO4 and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WPP OCA].
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*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structural studies of metal ions in family II pyrophosphatases: the requirement for a Janus ion., Fabrichniy IP, Lehtio L, Salminen A, Zyryanov AB, Baykov AA, Lahti R, Goldman A, Biochemistry. 2004 Nov 16;43(45):14403-11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15533045 15533045]
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[[Category: Large Structures]]
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[[Category: Inorganic diphosphatase]]
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[[Category: Streptococcus gordonii str. Challis]]
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[[Category: Single protein]]
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[[Category: Baykov AA]]
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[[Category: Streptococcus gordonii str. challis]]
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[[Category: Fabrichniy IP]]
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[[Category: Baykov, A.A.]]
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[[Category: Goldman A]]
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[[Category: Fabrichniy, I.P.]]
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[[Category: Lahti R]]
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[[Category: Goldman, A.]]
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[[Category: Lehtio L]]
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[[Category: Lahti, R.]]
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[[Category: Salminen A]]
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[[Category: Lehtio, L.]]
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[[Category: Salminen, A.]]
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[[Category: CL]]
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[[Category: SO4]]
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[[Category: ZN]]
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[[Category: inhibition]]
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[[Category: inorganic pyrophosphatase]]
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[[Category: metal binding]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:35:22 2007''
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Current revision

Structure of Streptococcus gordonii inorganic pyrophosphatase

PDB ID 1wpp

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